It would be helpful if mods could annotate user flags. For example, if a user submits a flag, I'll either address the issue or I'll dismiss it as invalid. Sometimes the issue is in a gray area, and the best thing to do is to wait and keep an eye on the situation; in that case, if would be helpful if I could leave a few words for the other mods.

(The ability to archive flags would also be helpful, and for similar reasons, but that's another issue!)

Yes, sometimes email or chat are the best way to handle a situation, but email can take a lot of time, and all the mods on a site aren't always online at the same time. Having the ability to annotate a flag would not only be convenient, it could be helpful to future mods. It would also help mods act more as a team.